[package - head-amd64-default][biology/muscle] Failed for muscle-3.8.1551 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Jan 14 12:57:46 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: mzaki at e-mail.ne.jp
Last committer: fernape at FreeBSD.org
Ident: $FreeBSD: head/biology/muscle/Makefile 522911 2020-01-13 17:42:22Z fernape $
Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p522982_s356710/logs/muscle-3.8.1551.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p522982_s356710
Log:
=>> Building biology/muscle
build started at Tue Jan 14 12:57:21 UTC 2020
port directory: /usr/ports/biology/muscle
package name: muscle-3.8.1551
building for: FreeBSD head-amd64-default-job-06 13.0-CURRENT FreeBSD 13.0-CURRENT 1300076 amd64
maintained by: mzaki at e-mail.ne.jp
Makefile ident: $FreeBSD: head/biology/muscle/Makefile 522911 2020-01-13 17:42:22Z fernape $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300062
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Job Id: 06
!!! Jail is newer than host. (Jail: 1300076, Host: 1300062) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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mzaki at e-mail.ne.jp
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=======================<phase: check-sanity >============================
===> License PD accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.12.0.txz
[head-amd64-default-job-06] Installing pkg-1.12.0...
[head-amd64-default-job-06] Extracting pkg-1.12.0: .......... done
===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of muscle-3.8.1551
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License PD accepted by the user
=> muscle_src_3.8.1551.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz
muscle_src_3.8.1551.tar.gz 185 kB 973 kBps 00s
===> Fetching all distfiles required by muscle-3.8.1551 for building
===========================================================================
=======================<phase: checksum >============================
===> License PD accepted by the user
===> Fetching all distfiles required by muscle-3.8.1551 for building
=> SHA256 Checksum OK for muscle_src_3.8.1551.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License PD accepted by the user
===> Fetching all distfiles required by muscle-3.8.1551 for building
===> Extracting for muscle-3.8.1551
=> SHA256 Checksum OK for muscle_src_3.8.1551.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for muscle-3.8.1551
===> Converting DOS text files to UNIX text files
===> Applying FreeBSD patches for muscle-3.8.1551
===========================================================================
=======================<phase: build-depends >============================
===> muscle-3.8.1551 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_3.txz
[head-amd64-default-job-06] Installing gmake-4.2.1_3...
[head-amd64-default-job-06] `-- Installing gettext-runtime-0.20.1...
[head-amd64-default-job-06] | `-- Installing indexinfo-0.3.1...
[head-amd64-default-job-06] | `-- Extracting indexinfo-0.3.1: .... done
<snip>
alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
switch (Alpha)
^
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 cluster.cpp -o cluster.o
clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
switch (m_JoinStyle)
^
clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
switch (m_CentroidStyle)
^
clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
switch (m_JoinStyle)
^
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o
3 warnings generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 estring.cpp -o estring.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fasta.cpp -o fasta.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistmafft.cpp -o fastdistmafft.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 finddiags.cpp -o finddiags.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch]
switch (g_PPScore)
^
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalsosx.cpp -o globalsosx.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msa.cpp -o msa.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o
msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
switch (Method)
^
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscore.cpp -o objscore.o
objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch]
switch (OS)
^
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscore2.cpp -o objscore2.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o
objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
switch (g_TermGaps)
^
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o
params.cpp:441:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
switch (g_PPScore)
^
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy3.cpp -o phy3.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o
In file included from profdb.cpp:9:
In file included from ./clustsetmsa.h:8:
./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
switch(m_Distance)
^
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o
profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
switch (g_Alpha)
^
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o
In file included from refine.cpp:9:
In file included from ./clustsetmsa.h:8:
./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
switch(m_Distance)
^
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o
seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference]
return (Seq &) *((Seq *) 0);
^~~~~~~~~~~~
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o
1 warning generated.
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o
c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 subfams.cpp -o subfams.o
subfams.cpp:4:13: error: functions that differ only in their return type cannot be overloaded
const float INFINITY = float(1e29);
~~~~~ ^
/usr/include/math.h:58:18: note: expanded from macro 'INFINITY'
#define INFINITY __builtin_inff()
^
subfams.cpp:4:13: note: previous implicit declaration is here
/usr/include/math.h:58:18: note: expanded from macro 'INFINITY'
#define INFINITY __builtin_inff()
^
1 error generated.
gmake[1]: *** [Makefile:32: subfams.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/muscle/work/muscle-3.8.1551'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/muscle
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